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Microbial Genomics logo Microbial Genomics

Volume 7, Issue 11

Genome-wide association study of gastric cancer- and duodenal ulcer-derived strains reveals discriminatory genetic variations and novel oncoprotein candidates Open Access

Abstract

Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as , which causes gastric cancer. We conducted a small-sample GWAS (125 gastric cancer cases and 115 controls) followed by prediction of gastric cancer and control (duodenal ulcer) strains. We identified 11 single nucleotide polymorphisms (eight amino acid changes) and three DNA motifs that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into gastric cancer pathogenesis and a basis for identifying a set of biomarkers for distinguishing these -related diseases.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): duodenal ulcer , gastric cancer , GWAS , Helicobacter pylori , population genomics and recombination
Funding
This study was supported by the:
  • ministry of education, culture, sports, science and technology (Award 18KK0266)
    • Principal Award Recipient: YoshioYamaoka
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.

Erratum

A correction has been published for this content:
Corrigendum: ‘Genome-wide association study of gastric cancer- and duodenal ulcer-derived strains reveals discriminatory genetic variations and novel oncoprotein candidates’
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2021-11-30
2026-02-10

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Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates
M Gen 7, 000680 (2021); https://doi.org/10.1099/mgen.0.000680
/content/journal/mgen/10.1099/mgen.0.000680
/content/journal/mgen/10.1099/mgen.0.000680
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